In the "Save As" dialog box, when you have chosen .PDF as the file type, click on the "Options" button near the bottom. When the Export Options dialog box opens, check the box at the top for "Export PDF in color". If this doesn't answer your question, please elaborate.

Not sure if there is direct option. You may save file as DWG/DXF and export layers with them. Now open DXF/DWG and print PDF from that and see if there any option to export layers. You will have to use Adobe illustrator to do this.